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1. Imprint of trace dissolved oxygen on prokaryoplankton community structure in an oxygen minimum zone

   https://doi.org/doi:10.3389/fmars.2020.00360  

   Medina Faull, L. ; Mara, Paraskevi ; Taylor, G.T. ; Edgcomb, V.P. ( January 2020 , Frontiers in marine science)

   null (Ed.)

   The Eastern Tropical North Pacific (ETNP) is a large, persistent, and intensifying oxygen minimum zone (OMZ) that accounts for almost half of the total area of global OMZs. Within the OMZ core (350–700 m depth), dissolved oxygen is typically near or below the analytical detection limit of modern sensors (10 nM). Steep oxygen gradients above and below the OMZ core lead to vertical structuring of microbial communities that also vary between particle-associated (PA) and free-living (FL) size fractions. Here, we use 16S amplicon sequencing (iTags) to analyze the diversity and distribution of prokaryotic populations between FL and PA size fractions and among the range of ambient redox conditions. The hydrographic conditions at our study area were distinct from those previously reported in the ETNP and other OMZs, such as the ETSP. Trace oxygen concentrations (0.35 mM) were present throughout the OMZ core at our sampling location. Consequently, nitrite accumulations typically reported for OMZ cores were absent as were sequences for anammox bacteria (Brocadiales genus Candidatus Scalindua), which are commonly found across oxic-anoxic boundaries in other systems. However, ammonia-oxidizing bacteria (AOB) and archaea (AOA) distributions and maximal autotrophic carbon assimilation rates (1.4 mM C d􀀀1) coincided with a pronounced ammonium concentration maximum near the top of the OMZ core. In addition, members of the genus Nitrospina, a dominant nitrite-oxidizing bacterial (NOB) clade were present suggesting that both ammonia and nitrite oxidation occur at trace oxygen concentrations. Analysis of similarity test (ANOSIM) and Non-metric Dimensional Scaling (nMDS) revealed that bacterial and archaeal phylogenetic representations were significantly different between size fractions. Based on ANOSIM and iTag profiles, composition of PA assemblages was less influenced by the prevailing depth-dependent biogeochemical regime than the FL fraction. Based on the presence of AOA, NOB and trace oxygen in the OMZ core we suggest that nitrification is an active process in the nitrogen cycle of this region of the ETNP OMZ. 

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2. Anaerobic methane oxidation is an important sink for methane in the ocean's largest oxygen minimum zone

   https://doi.org/10.1002/lno.11235  

   Thamdrup, Bo ; Steinsdóttir, Herdís G. R. ; Bertagnolli, Anthony D. ; Padilla, Cory C. ; Patin, Nastassia V. ; Garcia‐Robledo, Emilio ; Bristow, Laura A. ; Stewart, Frank J. ( June 2019 , Limnology and Oceanography)

   We investigated methane oxidation in the oxygen minimum zone (OMZ) of the eastern tropical North Pacific (ETNP) off central Mexico. Methane concentrations in the anoxic core of the OMZ reached ~ 20 nmol L⁻¹at off shelf sites and 34 nmol L⁻¹at a shelf site. Rates of methane oxidation were determined in ship‐board incubations with³H‐labeled methane at O₂concentrations 0–75 nmol L⁻¹. In vertical profiles at off‐shelf stations, highest rates were found between the secondary nitrite maximum at ~ 130 m and the methane maximum at 300–400 m in the anoxic core. Methane oxidation was inhibited by addition of 1μmol L⁻¹oxygen, which, together with the depth distribution, indicated an anaerobic pathway. A coupling to nitrite reduction was further indicated by the inhibitory effect of the nitric oxide scavenger 2‐phenyl‐4,4,5,5‐tetramethylimidazoline‐1‐oxyl‐3‐oxide (PTIO). Metatranscriptomes from the anoxic OMZ core supported the likely involvement of nitrite‐reducing bacteria of the NC10 clade in anaerobic methane oxidation, but also indicated a potential role for nitrate‐reducing euryarchaeotal methane oxidizers (ANME‐2d). Gammaproteobacteria of the Methanococcales were further detected in both 16S rRNA gene amplicons and metatranscriptomes, but the role of these presumed obligately aerobic methane oxidizers in the anoxic OMZ core is unclear. Given available estimates of water residence time, the measured rates and rate constants (up to ~ 1 yr⁻¹) imply that anaerobic methane oxidation is a substantial methane sink in the ETNP OMZ and hence attenuates the emission of methane from this and possibly other OMZs.

    

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3. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

   https://doi.org/10.1038/s41396-020-00825-6  

   Gazitúa, M. Consuelo ; Vik, Dean R. ; Roux, Simon ; Gregory, Ann C. ; Bolduc, Benjamin ; Widner, Brittany ; Mulholland, Margaret R. ; Hallam, Steven J. ; Ulloa, Osvaldo ; Sullivan, Matthew B. ( November 2020 , The ISME Journal)

   Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

    

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4. Novel metagenome-assembled genomes involved in the nitrogen cycle from a Pacific oxygen minimum zone

   https://doi.org/10.1038/s43705-021-00030-2  

   Sun, Xin ; Ward, Bess B. ( December 2021 , ISME Communications)

   null (Ed.)

   Abstract Oxygen minimum zones (OMZs) are unique marine regions where broad redox gradients stimulate biogeochemical cycles. Despite the important and unique role of OMZ microbes in these cycles, they are less characterized than microbes from the oxic ocean. Here we recovered 39 high- and medium-quality metagenome-assembled genomes (MAGs) from the Eastern Tropical South Pacific OMZ. More than half of these MAGs were not represented at the species level among 2631 MAGs from global marine datasets. OMZ MAGs were dominated by denitrifiers catalyzing nitrogen loss and especially MAGs with partial denitrification metabolism. A novel bacterial genome with nitrate-reducing potential could only be assigned to the phylum level. A Marine-Group II archaeon was found to be a versatile denitrifier, with the potential capability to respire multiple nitrogen compounds including N 2 O. The newly discovered denitrifying MAGs will improve our understanding of microbial adaptation strategies and the evolution of denitrification in the tree of life. 

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5. All about nitrite: exploring nitrite sources and sinks in the eastern tropical North Pacific oxygen minimum zone

   https://doi.org/10.5194/bg-20-2499-2023  

   Tracey, John C. ; Babbin, Andrew R. ; Wallace, Elizabeth ; Sun, Xin ; DuRussel, Katherine L. ; Frey, Claudia ; Martocello III, Donald E. ; Tamasi, Tyler ; Oleynik, Sergey ; Ward, Bess B. ( January 2023 , Biogeosciences)

   Abstract. Oxygen minimum zones (OMZs), due to their large volumes of perennially deoxygenated waters, are critical regions for understanding how the interplay between anaerobic and aerobic nitrogen (N) cycling microbial pathways affects the marine N budget. Here, we present a suite of measurements of the most significant OMZ N cycling rates, which all involve nitrite (NO2-) as a product, reactant, or intermediate, in the eastern tropical North Pacific (ETNP) OMZ. These measurements and comparisons to data from previously published OMZ cruisespresent additional evidence that NO3- reduction is the predominant OMZ N flux, followed by NO2- oxidation back to NO3-. The combined rates of both of these N recycling processes were observed to be much greater (up to nearly 200 times) thanthe combined rates of the N loss processes of anammox and denitrification, especially in waters near the anoxic–oxic interface. We also showthat NO2- oxidation can occur when O2 is maintained near 1 nM by a continuous-purge system, NO2-oxidation and O2 measurements that further strengthen the case for truly anaerobic NO2- oxidation. We also evaluate thepossibility that NO2- dismutation provides the oxidative power for anaerobic NO2- oxidation. The partitioning ofN loss between anammox and denitrification differed widely from stoichiometric predictions of at most 29 % anammox; in fact,N loss rates at many depths were entirely due to anammox. Our new NO3- reduction, NO2- oxidation, dismutation, andN loss data shed light on many open questions in OMZ N cycling research, especially the possibility of truly anaerobicNO2- oxidation.

    

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